6-Arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of bacterial D-alanine:D-alanine ligase

PLoS One. 2012;7(8):e39922. doi: 10.1371/journal.pone.0039922. Epub 2012 Aug 2.


Background: ATP-dependent D-alanine:D-alanine ligase (Ddl) is a part of biochemical machinery involved in peptidoglycan biosynthesis, as it catalyzes the formation of the terminal D-ala-D-ala dipeptide of the peptidoglycan precursor UDPMurNAc-pentapeptide. Inhibition of Ddl prevents bacterial growth, which makes this enzyme an attractive and viable target in the urgent search of novel effective antimicrobial drugs. To address the problem of a relentless increase in resistance to known antimicrobial agents we focused our attention to discovery of novel ATP-competitive inhibitors of Ddl.

Methodology/principal findings: Encouraged by recent successful attempts to find selective ATP-competitive inhibitors of bacterial enzymes we designed, synthesized and evaluated a library of 6-arylpyrido[2,3-d]pyrimidine-based compounds as inhibitors of Escherichia coli DdlB. Inhibitor binding to the target enzyme was subsequently confirmed by surface plasmon resonance and studied with isothermal titration calorimetry. Since kinetic analysis indicated that 6-arylpyrido[2,3-d]pyrimidines compete with the enzyme substrate ATP, inhibitor binding to the ATP-binding site was additionally studied with docking. Some of these inhibitors were found to possess antibacterial activity against membrane-compromised and efflux pump-deficient strains of E. coli.

Conclusions/significance: We discovered new ATP-competitive inhibitors of DdlB, which may serve as a starting point for development of more potent inhibitors of DdlB that could include both, an ATP-competitive and D-Ala competitive moiety.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • Escherichia coli / drug effects*
  • Escherichia coli / enzymology*
  • Inhibitory Concentration 50
  • Microbial Sensitivity Tests
  • Molecular Docking Simulation
  • Peptide Synthases / antagonists & inhibitors*
  • Peptide Synthases / chemistry
  • Peptide Synthases / metabolism
  • Protein Binding
  • Pyrimidines / chemistry
  • Pyrimidines / pharmacology*
  • Thermodynamics


  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • Pyrimidines
  • Adenosine Triphosphate
  • Peptide Synthases
  • D-alanylalanine synthetase

Grant support

This work was supported by the Slovenian Research Agency (Grant P1-0208). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.